The challenges of investigating groundwater ecosystems using boreholes

Groundwater ecosystems remain poorly understood yet may provide vital ecosystem services, contain useful bio-indicators of water quality, and make a unique contribution to biodiversity. The limited understanding of these ecosystems is a result of the inaccessibility of the subsurface habitat. Boreholes provide the main sampling window into deeper non-karstic aquifers and are commonly used to investigate bacterial and invertebrate communities. We investigated the differences between borehole and aquifer hydrochemistry, bacteria, and invertebrates at different depths beneath the surface. Packers were deployed to isolate three potential aquifer habitats (fractures/conduits) intercepted by two Chalk boreholes. Hydrochemical, microbiology and invertebrates samples were then taken progressively with pumping to assess differences between borehole and aquifer communities. Invertebrate net samples were also taken from the boreholes. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. Moreover, there was also evidence that the bacterial community structure differed between the borehole and the aquifer. Therefore this study demonstrates the challenges of assessing bacterial and invertebrate abundance within aquifers by using boreholes, which has implications for assessing the significance of their ecosystem services provision.